3-103794592-C-T

Variant names:

• chr3-103794592-C-T
• rs1673866

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.279 in 151,392 control chromosomes in the GnomAD database, including 6,688 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.28 (6688 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42268 AN: 151274 Hom.: 6689 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.343

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.279 AC: 42262 AN: 151392 Hom.: 6688 Cov.: 32 AF XY: 0.275 AC XY: 20306 AN XY: 73950

African (AFR) AF: 0.147 AC: 6107 AN: 41422

American (AMR) AF: 0.299 AC: 4529 AN: 15128

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1527 AN: 3446

East Asian (EAS) AF: 0.141 AC: 724 AN: 5128

South Asian (SAS) AF: 0.213 AC: 1026 AN: 4818

European-Finnish (FIN) AF: 0.307 AC: 3241 AN: 10554

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24002 AN: 67590

Other (OTH) AF: 0.339 AC: 713 AN: 2104

Alfa AF: 0.317 Hom.: 16198

Bravo AF: 0.276

Asia WGS AF: 0.131 AC: 457 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	13
DANN	Benign	0.54
PhyloP100		1.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1673866;

hg19: chr3-103513436;